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Reference documentation for deal.II version 9.6.0
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Reference documentation for deal.II version 9.6.0
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#include <deal.II/lac/petsc_block_vector.h>
Public Types | |
| using | BaseClass = BlockVectorBase<Vector> |
| using | BlockType = BaseClass::BlockType |
| using | value_type = BaseClass::value_type |
| using | pointer = BaseClass::pointer |
| using | const_pointer = BaseClass::const_pointer |
| using | reference = BaseClass::reference |
| using | const_reference = BaseClass::const_reference |
| using | size_type = BaseClass::size_type |
| using | iterator = BaseClass::iterator |
| using | const_iterator = BaseClass::const_iterator |
| using | real_type |
Public Member Functions | |
| BlockVector () | |
| BlockVector (const unsigned int n_blocks, const MPI_Comm communicator, const size_type block_size, const size_type locally_owned_size) | |
| BlockVector (const BlockVector &V) | |
| BlockVector (const std::vector< size_type > &block_sizes, const MPI_Comm communicator, const std::vector< size_type > &local_elements) | |
| BlockVector (const std::vector< IndexSet > ¶llel_partitioning, const MPI_Comm communicator=MPI_COMM_WORLD) | |
| BlockVector (const std::vector< IndexSet > ¶llel_partitioning, const std::vector< IndexSet > &ghost_indices, const MPI_Comm communicator) | |
| BlockVector (Vec v) | |
| template<size_t num_blocks> | |
| BlockVector (const std::array< Vec, num_blocks > &) | |
| ~BlockVector () override | |
| BlockVector & | operator= (const value_type s) |
| BlockVector & | operator= (const BlockVector &V) |
| void | reinit (Vec v) |
| void | reinit (const unsigned int n_blocks, const MPI_Comm communicator, const size_type block_size, const size_type locally_owned_size, const bool omit_zeroing_entries=false) |
| void | reinit (const std::vector< size_type > &block_sizes, const MPI_Comm communicator, const std::vector< size_type > &locally_owned_sizes, const bool omit_zeroing_entries=false) |
| void | reinit (const BlockVector &V, const bool omit_zeroing_entries=false) |
| void | reinit (const std::vector< IndexSet > ¶llel_partitioning, const MPI_Comm communicator) |
| void | reinit (const std::vector< IndexSet > ¶llel_partitioning, const std::vector< IndexSet > &ghost_entries, const MPI_Comm communicator) |
| void | reinit (const std::vector< std::shared_ptr< const Utilities::MPI::Partitioner > > &partitioners, const bool make_ghosted=true) |
| void | collect_sizes () |
| void | compress (VectorOperation::values operation) |
| void | reinit (const unsigned int num_blocks) |
| bool | has_ghost_elements () const |
| MPI_Comm | get_mpi_communicator () const |
| operator const Vec & () const | |
| Vec & | petsc_vector () |
| void | swap (BlockVector &v) |
| void | print (std::ostream &out, const unsigned int precision=3, const bool scientific=true, const bool across=true) const |
| BlockType & | block (const unsigned int i) |
| const BlockType & | block (const unsigned int i) const |
| const BlockIndices & | get_block_indices () const |
| unsigned int | n_blocks () const |
| virtual size_type | size () const override |
| std::size_t | locally_owned_size () const |
| IndexSet | locally_owned_elements () const |
| iterator | begin () |
| const_iterator | begin () const |
| iterator | end () |
| const_iterator | end () const |
| value_type | operator() (const size_type i) const |
| reference | operator() (const size_type i) |
| value_type | operator[] (const size_type i) const |
| reference | operator[] (const size_type i) |
| void | extract_subvector_to (const std::vector< size_type > &indices, std::vector< OtherNumber > &values) const |
| virtual void | extract_subvector_to (const ArrayView< const types::global_dof_index > &indices, ArrayView< value_type > &entries) const override |
| void | extract_subvector_to (ForwardIterator indices_begin, const ForwardIterator indices_end, OutputIterator values_begin) const |
| bool | operator== (const BlockVectorBase< VectorType2 > &v) const |
| value_type | operator* (const BlockVectorBase &V) const |
| real_type | norm_sqr () const |
| value_type | mean_value () const |
| real_type | l1_norm () const |
| real_type | l2_norm () const |
| real_type | linfty_norm () const |
| value_type | add_and_dot (const value_type a, const BlockVectorBase &V, const BlockVectorBase &W) |
| bool | in_local_range (const size_type global_index) const |
| bool | all_zero () const |
| bool | is_non_negative () const |
| BlockVectorBase & | operator+= (const BlockVectorBase &V) |
| BlockVectorBase & | operator-= (const BlockVectorBase &V) |
| void | add (const std::vector< size_type > &indices, const std::vector< Number > &values) |
| void | add (const std::vector< size_type > &indices, const Vector< Number > &values) |
| void | add (const size_type n_elements, const size_type *indices, const Number *values) |
| void | add (const value_type s) |
| void | add (const value_type a, const BlockVectorBase &V) |
| void | add (const value_type a, const BlockVectorBase &V, const value_type b, const BlockVectorBase &W) |
| void | sadd (const value_type s, const BlockVectorBase &V) |
| void | sadd (const value_type s, const value_type a, const BlockVectorBase &V) |
| void | sadd (const value_type s, const value_type a, const BlockVectorBase &V, const value_type b, const BlockVectorBase &W) |
| void | sadd (const value_type s, const value_type a, const BlockVectorBase &V, const value_type b, const BlockVectorBase &W, const value_type c, const BlockVectorBase &X) |
| BlockVectorBase & | operator*= (const value_type factor) |
| BlockVectorBase & | operator/= (const value_type factor) |
| void | scale (const BlockVector2 &v) |
| void | equ (const value_type a, const BlockVector2 &V) |
| void | update_ghost_values () const |
| std::size_t | memory_consumption () const |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
Subscriptor functionality | |
Classes derived from Subscriptor provide a facility to subscribe to this object. This is mostly used by the SmartPointer class. | |
| void | subscribe (std::atomic< bool > *const validity, const std::string &identifier="") const |
| void | unsubscribe (std::atomic< bool > *const validity, const std::string &identifier="") const |
| unsigned int | n_subscriptions () const |
| template<typename StreamType > | |
| void | list_subscribers (StreamType &stream) const |
| void | list_subscribers () const |
Static Public Member Functions | |
| static ::ExceptionBase & | ExcIteratorRangeDoesNotMatchVectorSize () |
| static ::ExceptionBase & | ExcNonMatchingBlockVectors () |
| static ::ExceptionBase & | ExcInUse (int arg1, std::string arg2, std::string arg3) |
| static ::ExceptionBase & | ExcNoSubscriber (std::string arg1, std::string arg2) |
Protected Attributes | |
| std::vector< Vector > | components |
| BlockIndices | block_indices |
Private Types | |
| using | map_value_type = decltype(counter_map)::value_type |
| using | map_iterator = decltype(counter_map)::iterator |
Private Member Functions | |
| void | setup_nest_vec () |
| void | check_no_subscribers () const noexcept |
Private Attributes | |
| Vec | petsc_nest_vector |
| std::atomic< unsigned int > | counter |
| std::map< std::string, unsigned int > | counter_map |
| std::vector< std::atomic< bool > * > | validity_pointers |
| const std::type_info * | object_info |
Static Private Attributes | |
| static std::mutex | mutex |
Related Symbols | |
(Note that these are not member symbols.) | |
| void | swap (BlockVector &u, BlockVector &v) |
An implementation of block vectors based on the parallel vector class implemented in PETScWrappers. While the base class provides for most of the interface, this class handles the actual allocation of vectors and provides functions that are specific to the underlying vector type.
The model of distribution of data is such that each of the blocks is distributed across all MPI processes named in the MPI communicator. I.e. we don't just distribute the whole vector, but each component. In the constructors and reinit() functions, one therefore not only has to specify the sizes of the individual blocks, but also the number of elements of each of these blocks to be stored on the local process.
Definition at line 60 of file petsc_block_vector.h.
Typedef the base class for simpler access to its own alias.
Definition at line 66 of file petsc_block_vector.h.
Typedef the type of the underlying vector.
Definition at line 71 of file petsc_block_vector.h.
Import the alias from the base class.
Definition at line 76 of file petsc_block_vector.h.
Definition at line 77 of file petsc_block_vector.h.
Definition at line 78 of file petsc_block_vector.h.
Definition at line 79 of file petsc_block_vector.h.
Definition at line 80 of file petsc_block_vector.h.
Definition at line 81 of file petsc_block_vector.h.
Definition at line 82 of file petsc_block_vector.h.
Definition at line 83 of file petsc_block_vector.h.
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inherited |
Declare a type that has holds real-valued numbers with the same precision as the template argument to this class. If the template argument of this class is a real data type, then real_type equals the template argument. If the template argument is a std::complex type then real_type equals the type underlying the complex numbers.
This alias is used to represent the return type of norms.
Definition at line 480 of file block_vector_base.h.
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privateinherited |
The data type used in counter_map.
Definition at line 229 of file subscriptor.h.
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privateinherited |
The iterator type used in counter_map.
Definition at line 234 of file subscriptor.h.
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inline |
Default constructor. Generate an empty vector without any blocks.
Definition at line 383 of file petsc_block_vector.h.
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inlineexplicit |
Constructor. Generate a block vector with n_blocks blocks, each of which is a parallel vector across communicator with block_size elements of which locally_owned_size elements are stored on the present process.
Definition at line 390 of file petsc_block_vector.h.
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inline |
Copy constructor. Set all the properties of the parallel vector to those of the given argument and copy the elements.
Definition at line 412 of file petsc_block_vector.h.
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inline |
Constructor. Set the number of blocks to block_sizes.size() and initialize each block with block_sizes[i] zero elements. The individual blocks are distributed across the given communicator, and each store local_elements[i] elements on the present process.
Definition at line 401 of file petsc_block_vector.h.
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inlineexplicit |
Create a BlockVector with parallel_partitioning.size() blocks, each initialized with the given IndexSet.
Definition at line 426 of file petsc_block_vector.h.
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inline |
Same as above, but include ghost elements
Definition at line 436 of file petsc_block_vector.h.
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inlineexplicit |
Create a BlockVector with a PETSc Vec It infers the number of blocks from the Vec if it is of type VECNEST, otherwise the block vector will only have a single block. Internally, we always store a VECNEST vector.
Definition at line 447 of file petsc_block_vector.h.
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inlineexplicit |
Create a BlockVector with an array of PETSc vectors.
Definition at line 456 of file petsc_block_vector.h.
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override |
Destructor. Clears memory
Definition at line 37 of file petsc_parallel_block_vector.cc.
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inline |
Copy operator: fill all components of the vector that are locally stored with the given scalar value.
Definition at line 470 of file petsc_block_vector.h.
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inline |
Copy operator for arguments of the same type. Resize the present vector if necessary to the correct number of blocks, then copy the individual blocks from v using the copy-assignment operator of the class that represents the individual blocks.
Copying the vectors that make up individual blocks can have complex semantics in parallel vector classes. See the information provided by the class used to represent the individual blocks.
Definition at line 479 of file petsc_block_vector.h.
| void BlockVector< Number >::reinit | ( | Vec | v | ) |
This method associates the PETSc Vec to the instance of the class. Infers the number of blocks from v if it is of type VECNEST, otherwise the block vector will only have a single block.
Definition at line 58 of file petsc_parallel_block_vector.cc.
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inline |
Reinitialize the BlockVector to contain n_blocks of size block_size, each of which stores locally_owned_size elements locally. The communicator argument denotes which MPI channel each of these blocks shall communicate.
If omit_zeroing_entries==false, the vector is filled with zeros.
Definition at line 501 of file petsc_block_vector.h.
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inline |
Reinitialize the BlockVector such that it contains block_sizes.size() blocks. Each block is reinitialized to dimension block_sizes[i]. Each of them stores locally_owned_sizes[i] elements on the present process.
If the number of blocks is the same as before this function was called, all vectors remain the same and reinit() is called for each vector.
If omit_zeroing_entries==false, the vector is filled with zeros.
Note that you must call this (or the other reinit() functions) function, rather than calling the reinit() functions of an individual block, to allow the block vector to update its caches of vector sizes. If you call reinit() of one of the blocks, then subsequent actions on this object may yield unpredictable results since they may be routed to the wrong block.
Definition at line 516 of file petsc_block_vector.h.
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inline |
Change the dimension to that of the vector V. The same applies as for the other reinit() function.
The elements of V are not copied, i.e. this function is the same as calling reinit (V.size(), omit_zeroing_entries).
Note that you must call this (or the other reinit() functions) function, rather than calling the reinit() functions of an individual block, to allow the block vector to update its caches of vector sizes. If you call reinit() on one of the blocks, then subsequent actions on this object may yield unpredictable results since they may be routed to the wrong block.
Definition at line 535 of file petsc_block_vector.h.
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inline |
Reinitialize the BlockVector using IndexSets. See the constructor with the same arguments for details.
Definition at line 550 of file petsc_block_vector.h.
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inline |
Same as above but include ghost entries.
Definition at line 568 of file petsc_block_vector.h.
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inline |
Initialize each block given to each parallel partitioning described in partitioners.
You can decide whether your vector will contain ghost elements with make_ghosted.
Definition at line 591 of file petsc_block_vector.h.
| void BlockVector< Number >::collect_sizes | ( | ) |
This function collects the sizes of the sub-objects and stores them in internal arrays, in order to be able to relay global indices into the vector to indices into the subobjects. You must call this function each time after you have changed the size of the sub-objects.
Definition at line 121 of file petsc_parallel_block_vector.cc.
| void BlockVector< Number >::compress | ( | VectorOperation::values | operation | ) |
Call the compress() function on all the subblocks of the vector and update the internal state of the nested PETSc vector.
See Compressing distributed objects for more information.
Definition at line 128 of file petsc_parallel_block_vector.cc.
| void BlockVector< Number >::reinit | ( | const unsigned int | num_blocks | ) |
Change the number of blocks to num_blocks. The individual blocks will get initialized with zero size, so it is assumed that the user resizes the individual blocks by herself in an appropriate way, and calls collect_sizes afterwards.
Definition at line 44 of file petsc_parallel_block_vector.cc.
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inline |
Return if this vector is a ghosted vector (and thus read-only).
Definition at line 619 of file petsc_block_vector.h.
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inline |
Return the underlying MPI communicator.
Definition at line 611 of file petsc_block_vector.h.
| BlockVector< Number >::operator const Vec & | ( | ) | const |
Conversion operator to gain access to the underlying PETSc type. If you do this, you cut this class off some information it may need, so this conversion operator should only be used if you know what you do. In particular, it should only be used for read-only operations into the vector.
Definition at line 115 of file petsc_parallel_block_vector.cc.
| Vec & BlockVector< Number >::petsc_vector | ( | ) |
Return a reference to the underlying PETSc type. It can be used to modify the underlying data, so use it only when you know what you are doing.
Definition at line 110 of file petsc_parallel_block_vector.cc.
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inline |
Swap the contents of this vector and the other vector v. One could do this operation with a temporary variable and copying over the data elements, but this function is significantly more efficient since it only swaps the pointers to the data of the two vectors and therefore does not need to allocate temporary storage and move data around.
Limitation: right now this function only works if both vectors have the same number of blocks. If needed, the numbers of blocks should be exchanged, too.
This function is analogous to the swap() function of all C++ standard containers. Also, there is a global function swap(u,v) that simply calls u.swap(v), again in analogy to standard functions.
Definition at line 632 of file petsc_block_vector.h.
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inline |
Print to a stream.
Definition at line 643 of file petsc_block_vector.h.
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private |
Utility to set up the VECNEST object
Definition at line 135 of file petsc_parallel_block_vector.cc.
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inherited |
Access to a single block.
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inherited |
Read-only access to a single block.
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inherited |
Return a reference on the object that describes the mapping between block and global indices. The use of this function is highly deprecated and it should vanish in one of the next versions
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inherited |
Number of blocks.
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overridevirtualinherited |
Return dimension of the vector. This is the sum of the dimensions of all components.
Implements ReadVector< Vector::value_type >.
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inherited |
Return local dimension of the vector. This is the sum of the local dimensions (i.e., values stored on the current processor) of all components.
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inherited |
Return an index set that describes which elements of this vector are owned by the current processor. Note that this index set does not include elements this vector may store locally as ghost elements but that are in fact owned by another processor. As a consequence, the index sets returned on different processors if this is a distributed vector will form disjoint sets that add up to the complete index set. Obviously, if a vector is created on only one processor, then the result would satisfy
For block vectors, this function returns the union of the locally owned elements of the individual blocks, shifted by their respective index offsets.
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inherited |
Return an iterator pointing to the first element.
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inherited |
Return an iterator pointing to the first element of a constant block vector.
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inherited |
Return an iterator pointing to the element past the end.
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inherited |
Return an iterator pointing to the element past the end of a constant block vector.
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inherited |
Access components, returns U(i).
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inherited |
Access components, returns U(i) as a writeable reference.
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inherited |
Access components, returns U(i).
Exactly the same as operator().
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inherited |
Access components, returns U(i) as a writeable reference.
Exactly the same as operator().
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inherited |
Instead of getting individual elements of a vector via operator(), this function allows getting a whole set of elements at once. The indices of the elements to be read are stated in the first argument, the corresponding values are returned in the second.
If the current vector is called v, then this function is the equivalent to the code
indices and values arrays must be identical.
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overridevirtualinherited |
Implements ReadVector< Vector::value_type >.
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inherited |
Instead of getting individual elements of a vector via operator(), this function allows getting a whole set of elements at once. In contrast to the previous function, this function obtains the indices of the elements by dereferencing all elements of the iterator range provided by the first two arguments, and puts the vector values into memory locations obtained by dereferencing a range of iterators starting at the location pointed to by the third argument.
If the current vector is called v, then this function is the equivalent to the code
values_begin as there are iterators between indices_begin and indices_end.
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inherited |
Check for equality of two block vector types. This operation is only allowed if the two vectors already have the same block structure.
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inherited |
\(U = U * V\): scalar product.
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inherited |
Return the square of the \(l_2\)-norm.
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inherited |
Return the mean value of the elements of this vector.
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inherited |
Return the \(l_1\)-norm of the vector, i.e. the sum of the absolute values.
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inherited |
Return the \(l_2\)-norm of the vector, i.e. the square root of the sum of the squares of the elements.
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inherited |
Return the maximum absolute value of the elements of this vector, which is the \(l_\infty\)-norm of a vector.
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inherited |
Performs a combined operation of a vector addition and a subsequent inner product, returning the value of the inner product. In other words, the result of this function is the same as if the user called
The reason this function exists is that this operation involves less memory transfer than calling the two functions separately on deal.II's vector classes (Vector<Number> and LinearAlgebra::distributed::Vector<double>). This method only needs to load three vectors, this, V, W, whereas calling separate methods means to load the calling vector this twice. Since most vector operations are memory transfer limited, this reduces the time by 25% (or 50% if W equals this).
For complex-valued vectors, the scalar product in the second step is implemented as \(\left<v,w\right>=\sum_i v_i \bar{w_i}\).
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inherited |
Return true if the given global index is in the local range of this processor. Asks the corresponding block.
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inherited |
Return whether the vector contains only elements with value zero. This function is mainly for internal consistency check and should seldom be used when not in debug mode since it uses quite some time.
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inherited |
Return true if the vector has no negative entries, i.e. all entries are zero or positive. This function is used, for example, to check whether refinement indicators are really all positive (or zero).
|
inherited |
Addition operator. Fast equivalent to U.add(1, V).
|
inherited |
Subtraction operator. Fast equivalent to U.add(-1, V).
|
inherited |
A collective add operation: This function adds a whole set of values stored in values to the vector components specified by indices.
|
inherited |
This is a second collective add operation. As a difference, this function takes a deal.II vector of values.
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inherited |
Take an address where n_elements are stored contiguously and add them into the vector. Handles all cases which are not covered by the other two add() functions above.
|
inherited |
\(U(0-DIM)+=s\). Addition of s to all components. Note that s is a scalar and not a vector.
|
inherited |
U+=a*V. Simple addition of a scaled vector.
|
inherited |
U+=a*V+b*W. Multiple addition of scaled vectors.
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inherited |
U=s*U+V. Scaling and simple vector addition.
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inherited |
U=s*U+a*V. Scaling and simple addition.
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inherited |
U=s*U+a*V+b*W. Scaling and multiple addition.
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inherited |
U=s*U+a*V+b*W+c*X. Scaling and multiple addition.
|
inherited |
Scale each element of the vector by a constant value.
|
inherited |
Scale each element of the vector by the inverse of the given value.
|
inherited |
Multiply each element of this vector by the corresponding element of v.
|
inherited |
U=a*V. Assignment.
|
inherited |
Update the ghost values by calling update_ghost_values for each block.
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inherited |
Determine an estimate for the memory consumption (in bytes) of this object.
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inherited |
Subscribes a user of the object by storing the pointer validity. The subscriber may be identified by text supplied as identifier.
Definition at line 135 of file subscriptor.cc.
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inherited |
Unsubscribes a user from the object.
identifier and the validity pointer must be the same as the one supplied to subscribe(). Definition at line 155 of file subscriptor.cc.
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inlineinherited |
Return the present number of subscriptions to this object. This allows to use this class for reference counted lifetime determination where the last one to unsubscribe also deletes the object.
Definition at line 300 of file subscriptor.h.
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inlineinherited |
List the subscribers to the input stream.
Definition at line 317 of file subscriptor.h.
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inherited |
List the subscribers to deallog.
Definition at line 203 of file subscriptor.cc.
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inlineinherited |
Read or write the data of this object to or from a stream for the purpose of serialization using the BOOST serialization library.
This function does not actually serialize any of the member variables of this class. The reason is that what this class stores is only who subscribes to this object, but who does so at the time of storing the contents of this object does not necessarily have anything to do with who subscribes to the object when it is restored. Consequently, we do not want to overwrite the subscribers at the time of restoring, and then there is no reason to write the subscribers out in the first place.
Definition at line 309 of file subscriptor.h.
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privatenoexceptinherited |
Check that there are no objects subscribing to this object. If this check passes then it is safe to destroy the current object. It this check fails then this function will either abort or print an error message to deallog (by using the AssertNothrow mechanism), but will not throw an exception.
Definition at line 52 of file subscriptor.cc.
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related |
Global function which overloads the default implementation of the C++ standard library which uses a temporary object. The function simply exchanges the data of the two vectors.
Definition at line 668 of file petsc_block_vector.h.
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private |
A PETSc Vec object that describes the entire block vector. Internally, this is done by creating a "nested" vector using PETSc's VECNEST object whose individual blocks are the blocks of this vector.
Definition at line 370 of file petsc_block_vector.h.
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protectedinherited |
Pointer to the array of components.
Definition at line 963 of file block_vector_base.h.
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protectedinherited |
Object managing the transformation between global indices and indices within the different blocks.
Definition at line 969 of file block_vector_base.h.
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mutableprivateinherited |
Store the number of objects which subscribed to this object. Initially, this number is zero, and upon destruction it shall be zero again (i.e. all objects which subscribed should have unsubscribed again).
The creator (and owner) of an object is counted in the map below if HE manages to supply identification.
We use the mutable keyword in order to allow subscription to constant objects also.
This counter may be read from and written to concurrently in multithreaded code: hence we use the std::atomic class template.
Definition at line 218 of file subscriptor.h.
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mutableprivateinherited |
In this map, we count subscriptions for each different identification string supplied to subscribe().
Definition at line 224 of file subscriptor.h.
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mutableprivateinherited |
In this vector, we store pointers to the validity bool in the SmartPointer objects that subscribe to this class.
Definition at line 240 of file subscriptor.h.
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mutableprivateinherited |
Pointer to the typeinfo object of this object, from which we can later deduce the class name. Since this information on the derived class is neither available in the destructor, nor in the constructor, we obtain it in between and store it here.
Definition at line 248 of file subscriptor.h.
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staticprivateinherited |
A mutex used to ensure data consistency when accessing the mutable members of this class. This lock is used in the subscribe() and unsubscribe() functions, as well as in list_subscribers().
Definition at line 271 of file subscriptor.h.
1.11.0